Starting phenix.real_space_refine on Fri Feb 6 22:41:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4m_48898/02_2026/9n4m_48898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4m_48898/02_2026/9n4m_48898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4m_48898/02_2026/9n4m_48898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4m_48898/02_2026/9n4m_48898.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4m_48898/02_2026/9n4m_48898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4m_48898/02_2026/9n4m_48898.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.049 sd= 1.292 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 160 5.16 5 Na 4 4.78 5 C 18076 2.51 5 N 4490 2.21 5 O 5308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28054 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "B" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "C" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "D" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 320 Unusual residues: {' NA': 4, 'NAG': 4, 'POV': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 250 Unusual residues: {'NAG': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 212 Unusual residues: {'NAG': 4, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 250 Unusual residues: {'NAG': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.56, per 1000 atoms: 0.23 Number of scatterers: 28054 At special positions: 0 Unit cell: (128.74, 149.24, 213.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 P 16 15.00 Na 4 11.00 O 5308 8.00 N 4490 7.00 C 18076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1004 " - " ASN A 67 " " NAG A1005 " - " ASN A 275 " " NAG A1006 " - " ASN A 546 " " NAG A1007 " - " ASN A 751 " " NAG B1003 " - " ASN B 67 " " NAG B1004 " - " ASN B 73 " " NAG B1005 " - " ASN B 412 " " NAG C1003 " - " ASN C 67 " " NAG C1004 " - " ASN C 275 " " NAG C1005 " - " ASN C 546 " " NAG C1006 " - " ASN C 751 " " NAG D1005 " - " ASN D 67 " " NAG D1006 " - " ASN D 73 " " NAG D1007 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 412 " " NAG G 1 " - " ASN B 275 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN B 546 " " NAG J 1 " - " ASN B 751 " " NAG K 1 " - " ASN C 378 " " NAG L 1 " - " ASN C 412 " " NAG M 1 " - " ASN D 275 " " NAG N 1 " - " ASN D 378 " " NAG O 1 " - " ASN D 546 " " NAG P 1 " - " ASN D 751 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.2 seconds 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6272 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 38 sheets defined 41.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.554A pdb=" N PHE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.799A pdb=" N SER A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.584A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.525A pdb=" N ARG A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.792A pdb=" N LEU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.630A pdb=" N MET A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 removed outlier: 3.737A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 334 removed outlier: 3.593A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 4.202A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.526A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.786A pdb=" N LEU A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 505' Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.144A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.680A pdb=" N GLY A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.663A pdb=" N ARG A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.559A pdb=" N PHE A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 618 " --> pdb=" O PHE A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 648 removed outlier: 4.077A pdb=" N TRP A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 660 removed outlier: 4.632A pdb=" N ALA A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.651A pdb=" N MET A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.571A pdb=" N ALA A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 676' Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.506A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.921A pdb=" N PHE A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 4.117A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.811A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 780 " --> pdb=" O ASP A 776 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 794 through 799 removed outlier: 3.529A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.979A pdb=" N ILE A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 853 removed outlier: 3.508A pdb=" N LEU A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 853 " --> pdb=" O ASN A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.771A pdb=" N MET A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.545A pdb=" N ALA B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.594A pdb=" N CYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.713A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.942A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.624A pdb=" N LEU B 182 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.567A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.663A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 removed outlier: 3.978A pdb=" N ALA B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.647A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.819A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 4.183A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.568A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.996A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.622A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 removed outlier: 3.830A pdb=" N LEU B 559 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 560 " --> pdb=" O ASN B 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 560' Processing helix chain 'B' and resid 561 through 572 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 633 through 660 removed outlier: 3.671A pdb=" N GLY B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 removed outlier: 3.915A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 710 removed outlier: 3.886A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 707 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.814A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 746 Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.523A pdb=" N THR B 779 " --> pdb=" O ARG B 775 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.534A pdb=" N LYS B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP B 799 " --> pdb=" O LYS B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 853 removed outlier: 3.776A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 851 " --> pdb=" O LYS B 847 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 853 " --> pdb=" O ASN B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.554A pdb=" N PHE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.799A pdb=" N SER C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.583A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.525A pdb=" N ARG C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.793A pdb=" N LEU C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.630A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 removed outlier: 3.737A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 removed outlier: 3.593A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 removed outlier: 4.202A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 364 " --> pdb=" O MET C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 474 removed outlier: 3.527A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.786A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 505' Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.145A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 576 removed outlier: 3.680A pdb=" N GLY C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 585 removed outlier: 3.663A pdb=" N ARG C 583 " --> pdb=" O PHE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 removed outlier: 3.560A pdb=" N PHE C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 635 through 648 removed outlier: 4.077A pdb=" N TRP C 641 " --> pdb=" O GLY C 637 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 660 removed outlier: 4.632A pdb=" N ALA C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 665 removed outlier: 3.651A pdb=" N MET C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 removed outlier: 3.572A pdb=" N ALA C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 671 through 676' Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.506A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS C 696 " --> pdb=" O THR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 712 removed outlier: 3.919A pdb=" N PHE C 708 " --> pdb=" O LYS C 704 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 731 removed outlier: 4.118A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 748 Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.811A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 780 " --> pdb=" O ASP C 776 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 784 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 794 through 799 removed outlier: 3.529A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 821 removed outlier: 3.979A pdb=" N ILE C 820 " --> pdb=" O GLY C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 853 removed outlier: 3.507A pdb=" N LEU C 831 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER C 834 " --> pdb=" O GLY C 830 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 840 " --> pdb=" O PHE C 836 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 851 " --> pdb=" O LYS C 847 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 853 " --> pdb=" O ASN C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 3.770A pdb=" N MET C 861 " --> pdb=" O PHE C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.545A pdb=" N ALA D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.595A pdb=" N CYS D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.713A pdb=" N VAL D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.942A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.624A pdb=" N LEU D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.567A pdb=" N LYS D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.663A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.978A pdb=" N ALA D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.647A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.819A pdb=" N LEU D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 4.183A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 364 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.568A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 507 removed outlier: 3.997A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.622A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 560 removed outlier: 3.829A pdb=" N LEU D 559 " --> pdb=" O LEU D 556 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER D 560 " --> pdb=" O ASN D 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 556 through 560' Processing helix chain 'D' and resid 561 through 572 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 632 No H-bonds generated for 'chain 'D' and resid 630 through 632' Processing helix chain 'D' and resid 633 through 660 removed outlier: 3.672A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP D 641 " --> pdb=" O GLY D 637 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 647 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 696 removed outlier: 3.916A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 710 removed outlier: 3.886A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 707 " --> pdb=" O ASP D 703 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.814A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 746 Processing helix chain 'D' and resid 774 through 788 removed outlier: 3.523A pdb=" N THR D 779 " --> pdb=" O ARG D 775 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.533A pdb=" N LYS D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP D 799 " --> pdb=" O LYS D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 853 removed outlier: 3.776A pdb=" N VAL D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 851 " --> pdb=" O LYS D 847 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 853 " --> pdb=" O ASN D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 867 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 removed outlier: 7.502A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.233A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.578A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 400 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.637A pdb=" N ALA A 515 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY A 765 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.573A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 753 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 removed outlier: 5.702A pdb=" N ALA A 684 " --> pdb=" O VAL A 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 36 through 42 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 131 Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.244A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 175 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 278 through 280 removed outlier: 3.598A pdb=" N ARG B 280 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB6, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 491 removed outlier: 3.577A pdb=" N ALA B 490 " --> pdb=" O ASN B 499 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 499 " --> pdb=" O ALA B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AC1, first strand: chain 'B' and resid 737 through 738 removed outlier: 3.994A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 37 through 39 removed outlier: 7.502A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.233A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC5, first strand: chain 'C' and resid 202 through 203 removed outlier: 3.578A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 400 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 434 through 435 Processing sheet with id=AC7, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC8, first strand: chain 'C' and resid 513 through 515 removed outlier: 4.637A pdb=" N ALA C 515 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY C 765 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.572A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 753 " --> pdb=" O TYR C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 684 through 685 removed outlier: 5.702A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 36 through 42 Processing sheet with id=AD3, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AD4, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.244A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 175 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 278 through 280 removed outlier: 3.598A pdb=" N ARG D 280 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD7, first strand: chain 'D' and resid 432 through 433 Processing sheet with id=AD8, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD9, first strand: chain 'D' and resid 489 through 491 removed outlier: 3.577A pdb=" N ALA D 490 " --> pdb=" O ASN D 499 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN D 499 " --> pdb=" O ALA D 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE2, first strand: chain 'D' and resid 737 through 738 removed outlier: 3.993A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4440 1.31 - 1.44: 7639 1.44 - 1.56: 16232 1.56 - 1.68: 51 1.68 - 1.81: 272 Bond restraints: 28634 Sorted by residual: bond pdb=" C ASN B 557 " pdb=" N PRO B 558 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.91e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C ASN D 557 " pdb=" N PRO D 558 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.86e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.511 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C ASN A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.337 1.392 -0.056 1.11e-02 8.12e+03 2.51e+01 ... (remaining 28629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 36109 2.51 - 5.01: 2020 5.01 - 7.52: 324 7.52 - 10.03: 87 10.03 - 12.53: 64 Bond angle restraints: 38604 Sorted by residual: angle pdb=" N ILE C 742 " pdb=" CA ILE C 742 " pdb=" C ILE C 742 " ideal model delta sigma weight residual 113.47 105.80 7.67 1.01e+00 9.80e-01 5.76e+01 angle pdb=" N ILE A 742 " pdb=" CA ILE A 742 " pdb=" C ILE A 742 " ideal model delta sigma weight residual 113.47 105.84 7.63 1.01e+00 9.80e-01 5.71e+01 angle pdb=" C LEU C 85 " pdb=" N TYR C 86 " pdb=" CA TYR C 86 " ideal model delta sigma weight residual 121.54 133.20 -11.66 1.91e+00 2.74e-01 3.73e+01 angle pdb=" C LEU A 85 " pdb=" N TYR A 86 " pdb=" CA TYR A 86 " ideal model delta sigma weight residual 121.54 133.15 -11.61 1.91e+00 2.74e-01 3.69e+01 angle pdb=" N ALA D 263 " pdb=" CA ALA D 263 " pdb=" C ALA D 263 " ideal model delta sigma weight residual 114.75 107.37 7.38 1.26e+00 6.30e-01 3.43e+01 ... (remaining 38599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 16966 29.64 - 59.28: 695 59.28 - 88.92: 130 88.92 - 118.56: 92 118.56 - 148.20: 17 Dihedral angle restraints: 17900 sinusoidal: 8152 harmonic: 9748 Sorted by residual: dihedral pdb=" CA GLU C 808 " pdb=" C GLU C 808 " pdb=" N SER C 809 " pdb=" CA SER C 809 " ideal model delta harmonic sigma weight residual -180.00 -119.07 -60.93 0 5.00e+00 4.00e-02 1.49e+02 dihedral pdb=" CA GLU A 808 " pdb=" C GLU A 808 " pdb=" N SER A 809 " pdb=" CA SER A 809 " ideal model delta harmonic sigma weight residual -180.00 -119.10 -60.90 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA GLU B 811 " pdb=" C GLU B 811 " pdb=" N ALA B 812 " pdb=" CA ALA B 812 " ideal model delta harmonic sigma weight residual -180.00 -123.29 -56.71 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 17897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3702 0.084 - 0.168: 574 0.168 - 0.252: 46 0.252 - 0.336: 14 0.336 - 0.420: 4 Chirality restraints: 4340 Sorted by residual: chirality pdb=" C1 NAG C1005 " pdb=" ND2 ASN C 546 " pdb=" C2 NAG C1005 " pdb=" O5 NAG C1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C1 NAG A1006 " pdb=" ND2 ASN A 546 " pdb=" C2 NAG A1006 " pdb=" O5 NAG A1006 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C1 NAG D1007 " pdb=" ND2 ASN D 412 " pdb=" C2 NAG D1007 " pdb=" O5 NAG D1007 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 4337 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 267 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO A 268 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 267 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO C 268 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 227 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ILE B 227 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE B 227 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE B 228 " -0.020 2.00e-02 2.50e+03 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7129 2.80 - 3.32: 24255 3.32 - 3.85: 43678 3.85 - 4.37: 51161 4.37 - 4.90: 84863 Nonbonded interactions: 211086 Sorted by model distance: nonbonded pdb=" O PHE A 555 " pdb=" OH TYR A 651 " model vdw 2.270 3.040 nonbonded pdb=" O PHE C 555 " pdb=" OH TYR C 651 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR A 590 " pdb=" OD1 ASN A 605 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR C 590 " pdb=" OD1 ASN C 605 " model vdw 2.275 3.040 nonbonded pdb=" OG SER C 670 " pdb=" OD1 ASP C 672 " model vdw 2.299 3.040 ... (remaining 211081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 1002 or resid 1005)) selection = (chain 'B' and (resid 33 through 1002 or resid 1005)) selection = (chain 'C' and (resid 33 through 1002 or resid 1005)) selection = (chain 'D' and (resid 33 through 1002 or resid 1005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.560 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 28686 Z= 0.413 Angle : 1.452 25.332 38752 Z= 0.780 Chirality : 0.061 0.420 4340 Planarity : 0.008 0.113 4770 Dihedral : 18.796 148.205 11604 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 14.95 % Favored : 84.70 % Rotamer: Outliers : 0.21 % Allowed : 5.98 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.51 (0.09), residues: 3352 helix: -4.68 (0.05), residues: 1328 sheet: -4.26 (0.24), residues: 322 loop : -4.06 (0.11), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 384 TYR 0.038 0.002 TYR D 443 PHE 0.023 0.002 PHE B 735 TRP 0.022 0.003 TRP D 134 HIS 0.017 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00816 (28634) covalent geometry : angle 1.41027 (38604) SS BOND : bond 0.00316 ( 8) SS BOND : angle 0.67793 ( 16) hydrogen bonds : bond 0.31458 ( 746) hydrogen bonds : angle 10.81202 ( 2130) link_ALPHA1-3 : bond 0.01222 ( 2) link_ALPHA1-3 : angle 6.25609 ( 6) link_ALPHA1-6 : bond 0.00656 ( 2) link_ALPHA1-6 : angle 2.08963 ( 6) link_BETA1-4 : bond 0.01617 ( 14) link_BETA1-4 : angle 4.74170 ( 42) link_NAG-ASN : bond 0.01610 ( 26) link_NAG-ASN : angle 6.86843 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 824 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7074 (p90) cc_final: 0.6488 (p90) REVERT: A 120 SER cc_start: 0.8575 (t) cc_final: 0.8085 (t) REVERT: A 133 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7904 (tmt170) REVERT: A 134 TRP cc_start: 0.8297 (t60) cc_final: 0.7571 (t60) REVERT: A 137 GLN cc_start: 0.7880 (mt0) cc_final: 0.7417 (mt0) REVERT: A 247 MET cc_start: 0.6623 (mtt) cc_final: 0.6393 (mtm) REVERT: A 312 LEU cc_start: 0.7776 (mp) cc_final: 0.7573 (pp) REVERT: A 328 HIS cc_start: 0.7270 (m-70) cc_final: 0.7023 (m-70) REVERT: A 374 ARG cc_start: 0.8109 (ttp-170) cc_final: 0.7487 (ptt90) REVERT: A 399 LEU cc_start: 0.8067 (mm) cc_final: 0.7710 (mt) REVERT: A 479 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 521 TYR cc_start: 0.8501 (t80) cc_final: 0.8163 (t80) REVERT: A 562 ASP cc_start: 0.8419 (t0) cc_final: 0.8186 (t0) REVERT: A 584 PHE cc_start: 0.7218 (t80) cc_final: 0.6842 (t80) REVERT: A 587 TYR cc_start: 0.7921 (m-80) cc_final: 0.7672 (m-80) REVERT: A 748 ARG cc_start: 0.6856 (mpt-90) cc_final: 0.6398 (ttp-170) REVERT: A 793 MET cc_start: 0.7442 (mmm) cc_final: 0.7067 (mmt) REVERT: B 86 TYR cc_start: 0.7054 (m-80) cc_final: 0.6303 (m-80) REVERT: B 87 ASP cc_start: 0.7955 (m-30) cc_final: 0.6756 (m-30) REVERT: B 132 THR cc_start: 0.8825 (p) cc_final: 0.8489 (p) REVERT: B 133 ARG cc_start: 0.8145 (tmt-80) cc_final: 0.7679 (tpp80) REVERT: B 140 ASP cc_start: 0.7968 (m-30) cc_final: 0.7728 (t0) REVERT: B 308 ASP cc_start: 0.7472 (p0) cc_final: 0.7146 (t0) REVERT: B 400 GLU cc_start: 0.7673 (tt0) cc_final: 0.7317 (mm-30) REVERT: B 531 LYS cc_start: 0.7045 (mttm) cc_final: 0.6787 (mmtm) REVERT: B 536 LEU cc_start: 0.9204 (pp) cc_final: 0.8986 (pp) REVERT: B 589 TRP cc_start: 0.7778 (m100) cc_final: 0.7472 (m100) REVERT: B 708 PHE cc_start: 0.6671 (t80) cc_final: 0.5795 (m-80) REVERT: B 753 THR cc_start: 0.9090 (t) cc_final: 0.8788 (p) REVERT: C 42 PHE cc_start: 0.7044 (m-80) cc_final: 0.6820 (m-80) REVERT: C 80 THR cc_start: 0.8008 (p) cc_final: 0.7795 (t) REVERT: C 85 LEU cc_start: 0.7690 (mp) cc_final: 0.7220 (mt) REVERT: C 114 SER cc_start: 0.8836 (m) cc_final: 0.8480 (m) REVERT: C 152 ASP cc_start: 0.7541 (t0) cc_final: 0.7151 (t0) REVERT: C 157 SER cc_start: 0.8761 (m) cc_final: 0.8474 (p) REVERT: C 374 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7223 (ttp-110) REVERT: C 708 PHE cc_start: 0.7095 (t80) cc_final: 0.6264 (t80) REVERT: C 770 MET cc_start: 0.6162 (tpt) cc_final: 0.5863 (ttt) REVERT: C 815 LEU cc_start: 0.7684 (mt) cc_final: 0.7399 (mt) REVERT: C 818 GLN cc_start: 0.7321 (pt0) cc_final: 0.6932 (mm-40) REVERT: D 86 TYR cc_start: 0.7009 (m-80) cc_final: 0.6539 (m-80) REVERT: D 87 ASP cc_start: 0.7881 (m-30) cc_final: 0.6987 (m-30) REVERT: D 132 THR cc_start: 0.8635 (p) cc_final: 0.8352 (p) REVERT: D 166 PHE cc_start: 0.8395 (t80) cc_final: 0.8054 (t80) REVERT: D 308 ASP cc_start: 0.7413 (p0) cc_final: 0.7114 (p0) REVERT: D 345 LEU cc_start: 0.7220 (mm) cc_final: 0.6983 (tp) REVERT: D 350 HIS cc_start: 0.6723 (p90) cc_final: 0.6424 (p90) REVERT: D 360 MET cc_start: 0.8372 (tpt) cc_final: 0.7922 (tpp) REVERT: D 639 ILE cc_start: 0.7730 (mm) cc_final: 0.7326 (mt) REVERT: D 794 MET cc_start: 0.7917 (mtm) cc_final: 0.7205 (mtm) REVERT: D 842 PHE cc_start: 0.7666 (t80) cc_final: 0.7399 (t80) outliers start: 6 outliers final: 1 residues processed: 828 average time/residue: 0.1971 time to fit residues: 253.7262 Evaluate side-chains 443 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.3980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 141 ASN ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN B 81 GLN B 137 GLN B 141 ASN B 196 ASN B 367 HIS B 549 ASN B 747 GLN C 65 ASN C 98 GLN C 137 GLN C 141 ASN C 196 ASN ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 HIS D 81 GLN D 137 GLN D 141 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 GLN D 549 ASN D 792 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.205442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.173156 restraints weight = 36637.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.172843 restraints weight = 48309.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174363 restraints weight = 49613.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.175287 restraints weight = 31801.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.176372 restraints weight = 28109.157| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28686 Z= 0.157 Angle : 0.868 28.376 38752 Z= 0.417 Chirality : 0.049 0.412 4340 Planarity : 0.006 0.093 4770 Dihedral : 20.700 143.048 5226 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 2.80 % Allowed : 14.19 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.30 (0.11), residues: 3352 helix: -3.15 (0.09), residues: 1376 sheet: -4.05 (0.24), residues: 336 loop : -3.74 (0.13), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 354 TYR 0.014 0.002 TYR B 462 PHE 0.025 0.002 PHE D 59 TRP 0.049 0.002 TRP B 798 HIS 0.013 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00341 (28634) covalent geometry : angle 0.81124 (38604) SS BOND : bond 0.01176 ( 8) SS BOND : angle 1.54112 ( 16) hydrogen bonds : bond 0.04988 ( 746) hydrogen bonds : angle 5.72999 ( 2130) link_ALPHA1-3 : bond 0.01359 ( 2) link_ALPHA1-3 : angle 3.33629 ( 6) link_ALPHA1-6 : bond 0.01465 ( 2) link_ALPHA1-6 : angle 3.08360 ( 6) link_BETA1-4 : bond 0.00395 ( 14) link_BETA1-4 : angle 3.17634 ( 42) link_NAG-ASN : bond 0.01250 ( 26) link_NAG-ASN : angle 6.39772 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 509 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.6877 (OUTLIER) cc_final: 0.6125 (m-70) REVERT: A 78 TYR cc_start: 0.6859 (p90) cc_final: 0.6635 (p90) REVERT: A 134 TRP cc_start: 0.8040 (t60) cc_final: 0.7691 (t60) REVERT: A 196 ASN cc_start: 0.7102 (t0) cc_final: 0.6879 (t0) REVERT: A 200 LYS cc_start: 0.7273 (ttmt) cc_final: 0.6904 (tttt) REVERT: A 374 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7594 (ptt90) REVERT: A 380 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.7001 (t) REVERT: A 433 LEU cc_start: 0.6809 (mm) cc_final: 0.6459 (mt) REVERT: A 506 ILE cc_start: 0.5593 (mt) cc_final: 0.5284 (mt) REVERT: A 521 TYR cc_start: 0.8278 (t80) cc_final: 0.7658 (t80) REVERT: A 748 ARG cc_start: 0.7201 (mpt-90) cc_final: 0.6792 (ttm170) REVERT: A 872 GLN cc_start: 0.6258 (tm-30) cc_final: 0.5876 (tm-30) REVERT: B 41 ILE cc_start: 0.8545 (mm) cc_final: 0.8252 (mm) REVERT: B 123 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 133 ARG cc_start: 0.8243 (tmt-80) cc_final: 0.7965 (tpp80) REVERT: B 234 MET cc_start: 0.7831 (mmm) cc_final: 0.7460 (tpt) REVERT: B 308 ASP cc_start: 0.6791 (p0) cc_final: 0.6524 (p0) REVERT: B 536 LEU cc_start: 0.9079 (pp) cc_final: 0.8842 (pp) REVERT: B 589 TRP cc_start: 0.7867 (m100) cc_final: 0.7312 (m100) REVERT: B 645 LEU cc_start: 0.8303 (tp) cc_final: 0.8096 (tp) REVERT: B 753 THR cc_start: 0.9190 (t) cc_final: 0.8798 (p) REVERT: C 37 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6997 (ttm-80) REVERT: C 114 SER cc_start: 0.8307 (m) cc_final: 0.8050 (m) REVERT: C 323 MET cc_start: 0.8079 (tpt) cc_final: 0.7876 (tpp) REVERT: C 433 LEU cc_start: 0.7269 (mm) cc_final: 0.6915 (mt) REVERT: C 780 ILE cc_start: 0.8048 (mt) cc_final: 0.7806 (mt) REVERT: C 841 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6646 (tt0) REVERT: D 123 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.7632 (t0) REVERT: D 166 PHE cc_start: 0.8262 (t80) cc_final: 0.7930 (t80) REVERT: D 436 THR cc_start: 0.9057 (m) cc_final: 0.8854 (p) REVERT: D 611 SER cc_start: 0.8548 (m) cc_final: 0.8336 (m) outliers start: 82 outliers final: 42 residues processed: 568 average time/residue: 0.1678 time to fit residues: 155.2546 Evaluate side-chains 445 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 387 PHE Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain D residue 792 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 293 optimal weight: 0.6980 chunk 264 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 336 GLN ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 604 ASN D 328 HIS D 621 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.197447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.163944 restraints weight = 36785.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.166607 restraints weight = 61183.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167713 restraints weight = 47625.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168900 restraints weight = 30066.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.169948 restraints weight = 25661.403| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28686 Z= 0.200 Angle : 0.840 23.686 38752 Z= 0.404 Chirality : 0.049 0.449 4340 Planarity : 0.005 0.093 4770 Dihedral : 18.656 151.321 5226 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.35 % Favored : 85.53 % Rotamer: Outliers : 4.17 % Allowed : 15.15 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.12), residues: 3352 helix: -2.14 (0.12), residues: 1390 sheet: -3.86 (0.26), residues: 324 loop : -3.72 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 158 TYR 0.022 0.002 TYR D 86 PHE 0.030 0.002 PHE A 459 TRP 0.054 0.002 TRP B 798 HIS 0.025 0.002 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00470 (28634) covalent geometry : angle 0.79016 (38604) SS BOND : bond 0.00334 ( 8) SS BOND : angle 1.08839 ( 16) hydrogen bonds : bond 0.04376 ( 746) hydrogen bonds : angle 5.26436 ( 2130) link_ALPHA1-3 : bond 0.01708 ( 2) link_ALPHA1-3 : angle 3.33027 ( 6) link_ALPHA1-6 : bond 0.01461 ( 2) link_ALPHA1-6 : angle 2.40953 ( 6) link_BETA1-4 : bond 0.00517 ( 14) link_BETA1-4 : angle 3.29728 ( 42) link_NAG-ASN : bond 0.00945 ( 26) link_NAG-ASN : angle 5.84660 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 432 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6970 (p90) cc_final: 0.6711 (p90) REVERT: A 196 ASN cc_start: 0.7181 (t0) cc_final: 0.6965 (t0) REVERT: A 521 TYR cc_start: 0.8119 (t80) cc_final: 0.7642 (t80) REVERT: A 748 ARG cc_start: 0.7351 (mpt-90) cc_final: 0.6966 (ttm170) REVERT: A 793 MET cc_start: 0.6876 (mmm) cc_final: 0.6115 (mtt) REVERT: A 872 GLN cc_start: 0.6371 (tm-30) cc_final: 0.6160 (tm-30) REVERT: B 98 GLN cc_start: 0.7897 (tt0) cc_final: 0.7682 (tt0) REVERT: B 99 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8207 (mt) REVERT: B 123 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8100 (t0) REVERT: B 140 ASP cc_start: 0.6887 (t0) cc_final: 0.6662 (t0) REVERT: B 465 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6908 (t0) REVERT: B 480 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8111 (mt) REVERT: B 645 LEU cc_start: 0.8460 (tp) cc_final: 0.8253 (tp) REVERT: B 753 THR cc_start: 0.9279 (t) cc_final: 0.8876 (p) REVERT: B 758 LEU cc_start: 0.8680 (mm) cc_final: 0.8407 (mt) REVERT: C 85 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7026 (mp) REVERT: C 86 TYR cc_start: 0.7444 (m-80) cc_final: 0.7208 (m-80) REVERT: C 114 SER cc_start: 0.8429 (m) cc_final: 0.8223 (m) REVERT: D 123 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.7747 (t0) REVERT: D 187 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6742 (mt-10) REVERT: D 436 THR cc_start: 0.9201 (m) cc_final: 0.8924 (p) REVERT: D 459 PHE cc_start: 0.7558 (m-80) cc_final: 0.7192 (m-10) REVERT: D 589 TRP cc_start: 0.7407 (m100) cc_final: 0.7114 (m100) outliers start: 122 outliers final: 73 residues processed: 519 average time/residue: 0.1648 time to fit residues: 142.5152 Evaluate side-chains 464 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 384 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 387 PHE Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 178 optimal weight: 3.9990 chunk 222 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 276 optimal weight: 0.5980 chunk 199 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 184 optimal weight: 0.1980 chunk 127 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN B 621 GLN C 196 ASN C 417 GLN D 714 GLN D 792 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.201619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.169750 restraints weight = 36417.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.173553 restraints weight = 56560.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174018 restraints weight = 38784.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.175135 restraints weight = 27244.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175644 restraints weight = 24210.819| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28686 Z= 0.127 Angle : 0.779 22.793 38752 Z= 0.367 Chirality : 0.047 0.442 4340 Planarity : 0.005 0.088 4770 Dihedral : 17.529 160.825 5226 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 3.42 % Allowed : 17.37 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.13), residues: 3352 helix: -1.51 (0.13), residues: 1402 sheet: -3.62 (0.27), residues: 312 loop : -3.54 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 66 TYR 0.018 0.001 TYR D 86 PHE 0.023 0.001 PHE A 579 TRP 0.058 0.002 TRP B 798 HIS 0.011 0.001 HIS D 350 Details of bonding type rmsd covalent geometry : bond 0.00276 (28634) covalent geometry : angle 0.71977 (38604) SS BOND : bond 0.00785 ( 8) SS BOND : angle 1.15060 ( 16) hydrogen bonds : bond 0.03490 ( 746) hydrogen bonds : angle 4.86270 ( 2130) link_ALPHA1-3 : bond 0.01434 ( 2) link_ALPHA1-3 : angle 3.38472 ( 6) link_ALPHA1-6 : bond 0.01610 ( 2) link_ALPHA1-6 : angle 2.72448 ( 6) link_BETA1-4 : bond 0.00634 ( 14) link_BETA1-4 : angle 3.25436 ( 42) link_NAG-ASN : bond 0.00997 ( 26) link_NAG-ASN : angle 6.11682 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 434 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6920 (p90) cc_final: 0.6678 (p90) REVERT: A 245 MET cc_start: 0.6867 (tpp) cc_final: 0.6666 (tpp) REVERT: A 374 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7501 (ptt180) REVERT: A 521 TYR cc_start: 0.8174 (t80) cc_final: 0.7839 (t80) REVERT: A 748 ARG cc_start: 0.7339 (mpt-90) cc_final: 0.6819 (ttm170) REVERT: A 793 MET cc_start: 0.6898 (mmm) cc_final: 0.6345 (mtt) REVERT: B 98 GLN cc_start: 0.7822 (tt0) cc_final: 0.7589 (tt0) REVERT: B 123 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8191 (t0) REVERT: B 140 ASP cc_start: 0.7051 (t0) cc_final: 0.6799 (t0) REVERT: B 262 PHE cc_start: 0.6897 (t80) cc_final: 0.6563 (p90) REVERT: B 400 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7195 (mt-10) REVERT: B 443 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5088 (p90) REVERT: B 465 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6926 (t0) REVERT: B 536 LEU cc_start: 0.9176 (pp) cc_final: 0.8918 (pp) REVERT: B 758 LEU cc_start: 0.8638 (mm) cc_final: 0.8403 (mt) REVERT: C 114 SER cc_start: 0.8575 (m) cc_final: 0.8335 (m) REVERT: C 248 MET cc_start: 0.7127 (mmm) cc_final: 0.6498 (mmm) REVERT: C 670 SER cc_start: 0.8700 (p) cc_final: 0.8495 (p) REVERT: C 791 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7123 (mp) REVERT: D 123 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.7915 (t0) REVERT: D 436 THR cc_start: 0.9193 (m) cc_final: 0.8993 (p) REVERT: D 589 TRP cc_start: 0.7434 (m100) cc_final: 0.7208 (m100) outliers start: 100 outliers final: 53 residues processed: 504 average time/residue: 0.1536 time to fit residues: 128.1569 Evaluate side-chains 438 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 380 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 291 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A 604 ASN B 136 HIS ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.194261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.159896 restraints weight = 36748.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162742 restraints weight = 63531.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164085 restraints weight = 48942.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165096 restraints weight = 31104.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166574 restraints weight = 26372.627| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28686 Z= 0.203 Angle : 0.819 22.437 38752 Z= 0.387 Chirality : 0.049 0.459 4340 Planarity : 0.005 0.087 4770 Dihedral : 16.869 173.568 5226 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.98 % Favored : 84.93 % Rotamer: Outliers : 4.38 % Allowed : 17.92 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.13), residues: 3352 helix: -1.21 (0.13), residues: 1420 sheet: -3.78 (0.27), residues: 298 loop : -3.35 (0.13), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 66 TYR 0.019 0.002 TYR C 252 PHE 0.031 0.002 PHE C 359 TRP 0.069 0.002 TRP B 798 HIS 0.010 0.001 HIS D 350 Details of bonding type rmsd covalent geometry : bond 0.00481 (28634) covalent geometry : angle 0.76344 (38604) SS BOND : bond 0.00282 ( 8) SS BOND : angle 1.14115 ( 16) hydrogen bonds : bond 0.03771 ( 746) hydrogen bonds : angle 4.92834 ( 2130) link_ALPHA1-3 : bond 0.01199 ( 2) link_ALPHA1-3 : angle 3.37563 ( 6) link_ALPHA1-6 : bond 0.02095 ( 2) link_ALPHA1-6 : angle 2.38207 ( 6) link_BETA1-4 : bond 0.00493 ( 14) link_BETA1-4 : angle 3.42382 ( 42) link_NAG-ASN : bond 0.01004 ( 26) link_NAG-ASN : angle 6.08748 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 397 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7056 (p90) cc_final: 0.6770 (p90) REVERT: A 200 LYS cc_start: 0.7511 (ttmt) cc_final: 0.7236 (ttpt) REVERT: A 245 MET cc_start: 0.6916 (tpp) cc_final: 0.6709 (tpp) REVERT: A 257 THR cc_start: 0.8370 (m) cc_final: 0.8081 (p) REVERT: A 748 ARG cc_start: 0.7378 (mpt-90) cc_final: 0.6895 (ttm170) REVERT: A 793 MET cc_start: 0.7082 (mmm) cc_final: 0.6568 (mtt) REVERT: B 98 GLN cc_start: 0.7930 (tt0) cc_final: 0.7716 (tt0) REVERT: B 123 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8201 (t0) REVERT: B 187 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6734 (mt-10) REVERT: B 215 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7644 (mp) REVERT: B 443 TYR cc_start: 0.6782 (OUTLIER) cc_final: 0.5259 (p90) REVERT: B 465 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.6987 (t0) REVERT: B 569 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7051 (tp) REVERT: B 753 THR cc_start: 0.9293 (t) cc_final: 0.8932 (p) REVERT: B 758 LEU cc_start: 0.8912 (mm) cc_final: 0.8650 (mt) REVERT: C 114 SER cc_start: 0.8654 (m) cc_final: 0.8453 (m) REVERT: D 123 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.7932 (t0) REVERT: D 436 THR cc_start: 0.9214 (m) cc_final: 0.9010 (p) REVERT: D 443 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.5084 (p90) REVERT: D 569 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.6500 (tt) REVERT: D 589 TRP cc_start: 0.7493 (m100) cc_final: 0.7246 (m100) outliers start: 128 outliers final: 79 residues processed: 483 average time/residue: 0.1539 time to fit residues: 124.6199 Evaluate side-chains 464 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 377 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 861 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 387 PHE Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 275 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C 131 GLN C 196 ASN D 136 HIS ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.197429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.164628 restraints weight = 36652.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.166779 restraints weight = 60208.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167862 restraints weight = 49213.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168988 restraints weight = 30927.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170639 restraints weight = 26410.821| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28686 Z= 0.141 Angle : 0.762 22.066 38752 Z= 0.359 Chirality : 0.047 0.457 4340 Planarity : 0.005 0.086 4770 Dihedral : 16.259 177.180 5226 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 3.52 % Allowed : 19.43 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.14), residues: 3352 helix: -0.94 (0.13), residues: 1422 sheet: -3.55 (0.28), residues: 294 loop : -3.24 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.018 0.001 TYR D 86 PHE 0.025 0.001 PHE A 555 TRP 0.075 0.002 TRP D 798 HIS 0.009 0.001 HIS D 350 Details of bonding type rmsd covalent geometry : bond 0.00323 (28634) covalent geometry : angle 0.70529 (38604) SS BOND : bond 0.00241 ( 8) SS BOND : angle 0.77746 ( 16) hydrogen bonds : bond 0.03323 ( 746) hydrogen bonds : angle 4.67580 ( 2130) link_ALPHA1-3 : bond 0.01100 ( 2) link_ALPHA1-3 : angle 3.38993 ( 6) link_ALPHA1-6 : bond 0.01719 ( 2) link_ALPHA1-6 : angle 1.50802 ( 6) link_BETA1-4 : bond 0.00601 ( 14) link_BETA1-4 : angle 3.35907 ( 42) link_NAG-ASN : bond 0.00996 ( 26) link_NAG-ASN : angle 5.89658 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 401 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6988 (p90) cc_final: 0.6753 (p90) REVERT: A 241 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: A 257 THR cc_start: 0.8293 (m) cc_final: 0.8025 (p) REVERT: A 497 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: A 748 ARG cc_start: 0.7311 (mpt-90) cc_final: 0.6899 (ttm170) REVERT: A 793 MET cc_start: 0.6966 (mmm) cc_final: 0.6545 (mtt) REVERT: B 123 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8167 (t0) REVERT: B 166 PHE cc_start: 0.7569 (t80) cc_final: 0.7130 (t80) REVERT: B 187 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6735 (mt-10) REVERT: B 443 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.5090 (p90) REVERT: B 634 ARG cc_start: 0.7801 (mmt180) cc_final: 0.7530 (mmt180) REVERT: B 753 THR cc_start: 0.9272 (t) cc_final: 0.8945 (p) REVERT: B 758 LEU cc_start: 0.8869 (mm) cc_final: 0.8632 (mt) REVERT: C 114 SER cc_start: 0.8652 (m) cc_final: 0.8435 (m) REVERT: C 374 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7550 (ttp-110) REVERT: C 705 MET cc_start: 0.8256 (mmm) cc_final: 0.7758 (tpp) REVERT: D 123 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8083 (t0) REVERT: D 436 THR cc_start: 0.9232 (m) cc_final: 0.8962 (p) REVERT: D 443 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.5558 (p90) REVERT: D 627 MET cc_start: 0.7627 (mmt) cc_final: 0.7387 (mmt) outliers start: 103 outliers final: 66 residues processed: 475 average time/residue: 0.1520 time to fit residues: 120.9025 Evaluate side-chains 440 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 368 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 175 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 299 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 198 optimal weight: 0.1980 chunk 231 optimal weight: 0.0770 overall best weight: 2.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN D 819 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121814 restraints weight = 38176.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119633 restraints weight = 42963.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121011 restraints weight = 42678.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121501 restraints weight = 35687.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121488 restraints weight = 35317.022| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 28686 Z= 0.284 Angle : 0.885 22.337 38752 Z= 0.424 Chirality : 0.052 0.476 4340 Planarity : 0.005 0.084 4770 Dihedral : 16.164 161.123 5226 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.20 % Favored : 83.68 % Rotamer: Outliers : 4.45 % Allowed : 19.15 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.13), residues: 3352 helix: -1.06 (0.13), residues: 1432 sheet: -3.68 (0.28), residues: 298 loop : -3.30 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 66 TYR 0.020 0.002 TYR D 86 PHE 0.028 0.003 PHE B 735 TRP 0.083 0.003 TRP B 798 HIS 0.010 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00683 (28634) covalent geometry : angle 0.83353 (38604) SS BOND : bond 0.00225 ( 8) SS BOND : angle 1.08157 ( 16) hydrogen bonds : bond 0.04075 ( 746) hydrogen bonds : angle 5.15296 ( 2130) link_ALPHA1-3 : bond 0.01133 ( 2) link_ALPHA1-3 : angle 3.38085 ( 6) link_ALPHA1-6 : bond 0.01251 ( 2) link_ALPHA1-6 : angle 1.29598 ( 6) link_BETA1-4 : bond 0.00466 ( 14) link_BETA1-4 : angle 3.54278 ( 42) link_NAG-ASN : bond 0.00992 ( 26) link_NAG-ASN : angle 6.10144 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 396 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7261 (p90) cc_final: 0.6713 (p90) REVERT: A 241 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: A 497 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: A 565 MET cc_start: 0.7895 (tpp) cc_final: 0.7582 (tpt) REVERT: A 793 MET cc_start: 0.7372 (mmm) cc_final: 0.6831 (mtt) REVERT: B 123 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8297 (t0) REVERT: B 152 ASP cc_start: 0.7156 (t0) cc_final: 0.6704 (m-30) REVERT: B 187 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6949 (mt-10) REVERT: B 215 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7757 (mp) REVERT: B 262 PHE cc_start: 0.7447 (t80) cc_final: 0.6885 (p90) REVERT: B 443 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.5376 (p90) REVERT: B 620 MET cc_start: 0.8289 (tpp) cc_final: 0.8055 (mtt) REVERT: B 758 LEU cc_start: 0.9239 (mm) cc_final: 0.9033 (mt) REVERT: B 813 SER cc_start: 0.8366 (t) cc_final: 0.8080 (m) REVERT: C 114 SER cc_start: 0.8924 (m) cc_final: 0.8530 (t) REVERT: C 218 MET cc_start: 0.7708 (mmt) cc_final: 0.6241 (mtt) REVERT: D 123 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8163 (t0) REVERT: D 140 ASP cc_start: 0.7465 (t70) cc_final: 0.7250 (t70) REVERT: D 262 PHE cc_start: 0.7368 (t80) cc_final: 0.6865 (p90) REVERT: D 436 THR cc_start: 0.9166 (m) cc_final: 0.8928 (p) REVERT: D 443 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.5265 (p90) outliers start: 130 outliers final: 90 residues processed: 482 average time/residue: 0.1579 time to fit residues: 128.4564 Evaluate side-chains 466 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 369 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 735 PHE Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 42 optimal weight: 4.9990 chunk 287 optimal weight: 0.5980 chunk 206 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 308 optimal weight: 0.0570 chunk 271 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN B 491 GLN ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C 196 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.194548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.161156 restraints weight = 36856.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.164256 restraints weight = 60434.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.165367 restraints weight = 44801.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166031 restraints weight = 29797.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167810 restraints weight = 25697.719| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28686 Z= 0.139 Angle : 0.766 21.938 38752 Z= 0.362 Chirality : 0.047 0.462 4340 Planarity : 0.004 0.084 4770 Dihedral : 15.649 149.393 5226 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 3.25 % Allowed : 20.76 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.14), residues: 3352 helix: -0.71 (0.14), residues: 1418 sheet: -3.42 (0.27), residues: 316 loop : -3.16 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 374 TYR 0.022 0.001 TYR C 86 PHE 0.041 0.002 PHE C 555 TRP 0.050 0.002 TRP B 798 HIS 0.012 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00315 (28634) covalent geometry : angle 0.71043 (38604) SS BOND : bond 0.00762 ( 8) SS BOND : angle 0.75797 ( 16) hydrogen bonds : bond 0.03303 ( 746) hydrogen bonds : angle 4.71531 ( 2130) link_ALPHA1-3 : bond 0.01102 ( 2) link_ALPHA1-3 : angle 3.56909 ( 6) link_ALPHA1-6 : bond 0.01224 ( 2) link_ALPHA1-6 : angle 1.27956 ( 6) link_BETA1-4 : bond 0.00630 ( 14) link_BETA1-4 : angle 3.37279 ( 42) link_NAG-ASN : bond 0.01021 ( 26) link_NAG-ASN : angle 5.84949 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 389 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7073 (p90) cc_final: 0.6811 (p90) REVERT: A 198 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6904 (ttt90) REVERT: A 218 MET cc_start: 0.7135 (mmt) cc_final: 0.5965 (mmm) REVERT: A 241 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: A 565 MET cc_start: 0.7796 (tpp) cc_final: 0.7498 (tpt) REVERT: A 793 MET cc_start: 0.7099 (mmm) cc_final: 0.6702 (mtt) REVERT: B 123 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8145 (t0) REVERT: B 152 ASP cc_start: 0.7066 (t0) cc_final: 0.6637 (m-30) REVERT: B 187 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6920 (mt-10) REVERT: B 443 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.5522 (p90) REVERT: B 465 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6941 (t70) REVERT: B 590 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.5864 (p90) REVERT: B 758 LEU cc_start: 0.9112 (mm) cc_final: 0.8849 (mt) REVERT: C 87 ASP cc_start: 0.7638 (t0) cc_final: 0.6788 (t70) REVERT: C 114 SER cc_start: 0.8807 (m) cc_final: 0.8352 (t) REVERT: C 218 MET cc_start: 0.7429 (mmt) cc_final: 0.6100 (mmm) REVERT: C 705 MET cc_start: 0.8236 (mmm) cc_final: 0.7885 (tpp) REVERT: D 123 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8087 (t0) REVERT: D 436 THR cc_start: 0.9252 (m) cc_final: 0.8952 (p) REVERT: D 758 LEU cc_start: 0.9095 (mm) cc_final: 0.8806 (mt) outliers start: 95 outliers final: 73 residues processed: 454 average time/residue: 0.1615 time to fit residues: 123.3004 Evaluate side-chains 443 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 364 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 154 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 97 optimal weight: 0.0370 chunk 225 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 chunk 256 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.191241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.163066 restraints weight = 36146.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165318 restraints weight = 64375.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.166272 restraints weight = 51478.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.166969 restraints weight = 34642.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167861 restraints weight = 29445.562| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28686 Z= 0.150 Angle : 0.771 21.793 38752 Z= 0.364 Chirality : 0.048 0.469 4340 Planarity : 0.004 0.082 4770 Dihedral : 15.237 131.775 5226 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 3.39 % Allowed : 21.14 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.14), residues: 3352 helix: -0.59 (0.14), residues: 1420 sheet: -3.43 (0.27), residues: 318 loop : -3.11 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 374 TYR 0.030 0.001 TYR C 86 PHE 0.034 0.002 PHE C 555 TRP 0.082 0.002 TRP D 798 HIS 0.013 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00348 (28634) covalent geometry : angle 0.71717 (38604) SS BOND : bond 0.00457 ( 8) SS BOND : angle 0.73893 ( 16) hydrogen bonds : bond 0.03239 ( 746) hydrogen bonds : angle 4.66437 ( 2130) link_ALPHA1-3 : bond 0.00975 ( 2) link_ALPHA1-3 : angle 3.54337 ( 6) link_ALPHA1-6 : bond 0.01063 ( 2) link_ALPHA1-6 : angle 1.27580 ( 6) link_BETA1-4 : bond 0.00580 ( 14) link_BETA1-4 : angle 3.33442 ( 42) link_NAG-ASN : bond 0.00986 ( 26) link_NAG-ASN : angle 5.79635 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 382 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7037 (p90) cc_final: 0.6656 (p90) REVERT: A 198 ARG cc_start: 0.7495 (ttp80) cc_final: 0.6857 (ttt90) REVERT: A 218 MET cc_start: 0.7167 (mmt) cc_final: 0.6106 (mmm) REVERT: A 241 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: A 257 THR cc_start: 0.8422 (m) cc_final: 0.8053 (p) REVERT: A 374 ARG cc_start: 0.7959 (ttp-110) cc_final: 0.7535 (ptt90) REVERT: A 565 MET cc_start: 0.7776 (tpp) cc_final: 0.7487 (tpt) REVERT: A 779 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7134 (m) REVERT: A 793 MET cc_start: 0.7228 (mmm) cc_final: 0.6774 (mtt) REVERT: B 123 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 135 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7589 (ptmt) REVERT: B 152 ASP cc_start: 0.7223 (t0) cc_final: 0.6802 (m-30) REVERT: B 187 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6987 (mt-10) REVERT: B 443 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.5466 (p90) REVERT: B 590 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.5820 (p90) REVERT: B 758 LEU cc_start: 0.9155 (mm) cc_final: 0.8913 (mt) REVERT: C 87 ASP cc_start: 0.7653 (t0) cc_final: 0.7184 (t70) REVERT: C 114 SER cc_start: 0.8839 (m) cc_final: 0.8390 (t) REVERT: C 218 MET cc_start: 0.7359 (mmt) cc_final: 0.5991 (mtt) REVERT: D 123 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8260 (t0) REVERT: D 323 MET cc_start: 0.7909 (tpp) cc_final: 0.7534 (tpp) REVERT: D 436 THR cc_start: 0.9176 (m) cc_final: 0.8933 (p) REVERT: D 758 LEU cc_start: 0.9133 (mm) cc_final: 0.8856 (mt) outliers start: 99 outliers final: 77 residues processed: 447 average time/residue: 0.1588 time to fit residues: 117.7125 Evaluate side-chains 454 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 370 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 295 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 315 optimal weight: 0.0870 chunk 224 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 239 optimal weight: 0.0770 chunk 257 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 98 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.196218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.164432 restraints weight = 36313.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167998 restraints weight = 61605.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.168590 restraints weight = 41751.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169234 restraints weight = 30140.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171959 restraints weight = 25111.558| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28686 Z= 0.140 Angle : 0.764 21.740 38752 Z= 0.361 Chirality : 0.047 0.470 4340 Planarity : 0.005 0.082 4770 Dihedral : 14.964 130.506 5226 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 3.08 % Allowed : 21.61 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.14), residues: 3352 helix: -0.50 (0.14), residues: 1422 sheet: -3.35 (0.28), residues: 302 loop : -3.08 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 58 TYR 0.022 0.001 TYR C 86 PHE 0.033 0.002 PHE C 555 TRP 0.061 0.002 TRP D 798 HIS 0.016 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00321 (28634) covalent geometry : angle 0.71044 (38604) SS BOND : bond 0.00235 ( 8) SS BOND : angle 0.71233 ( 16) hydrogen bonds : bond 0.03155 ( 746) hydrogen bonds : angle 4.61657 ( 2130) link_ALPHA1-3 : bond 0.00912 ( 2) link_ALPHA1-3 : angle 3.52611 ( 6) link_ALPHA1-6 : bond 0.01028 ( 2) link_ALPHA1-6 : angle 1.28145 ( 6) link_BETA1-4 : bond 0.00596 ( 14) link_BETA1-4 : angle 3.33332 ( 42) link_NAG-ASN : bond 0.00998 ( 26) link_NAG-ASN : angle 5.72630 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6704 Ramachandran restraints generated. 3352 Oldfield, 0 Emsley, 3352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 375 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6842 (ttt90) REVERT: A 218 MET cc_start: 0.7009 (mmt) cc_final: 0.5924 (mmm) REVERT: A 241 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: A 257 THR cc_start: 0.8317 (m) cc_final: 0.8000 (p) REVERT: A 374 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7524 (ptt90) REVERT: A 565 MET cc_start: 0.7756 (tpp) cc_final: 0.7486 (tpt) REVERT: A 779 THR cc_start: 0.7179 (OUTLIER) cc_final: 0.6963 (m) REVERT: A 793 MET cc_start: 0.7097 (mmm) cc_final: 0.6687 (mtt) REVERT: B 123 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8171 (t0) REVERT: B 152 ASP cc_start: 0.7158 (t0) cc_final: 0.6762 (m-30) REVERT: B 187 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6963 (mt-10) REVERT: B 443 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5632 (p90) REVERT: B 590 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5716 (p90) REVERT: B 620 MET cc_start: 0.8407 (tpp) cc_final: 0.8121 (ttm) REVERT: B 758 LEU cc_start: 0.9106 (mm) cc_final: 0.8865 (mt) REVERT: C 87 ASP cc_start: 0.7595 (t0) cc_final: 0.7198 (t70) REVERT: C 114 SER cc_start: 0.8757 (m) cc_final: 0.8282 (t) REVERT: C 218 MET cc_start: 0.7183 (mmt) cc_final: 0.6265 (mtt) REVERT: C 705 MET cc_start: 0.8120 (mmm) cc_final: 0.7775 (tpp) REVERT: C 793 MET cc_start: 0.6887 (mmm) cc_final: 0.6136 (mtt) REVERT: D 123 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8102 (t0) REVERT: D 323 MET cc_start: 0.8111 (tpp) cc_final: 0.7910 (tpp) REVERT: D 436 THR cc_start: 0.9230 (m) cc_final: 0.8986 (p) REVERT: D 758 LEU cc_start: 0.9077 (mm) cc_final: 0.8811 (mt) outliers start: 90 outliers final: 72 residues processed: 434 average time/residue: 0.1594 time to fit residues: 116.0916 Evaluate side-chains 440 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 362 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 735 PHE Chi-restraints excluded: chain D residue 837 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 290 optimal weight: 0.2980 chunk 297 optimal weight: 0.9990 chunk 247 optimal weight: 0.1980 chunk 90 optimal weight: 0.0770 chunk 227 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 overall best weight: 0.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN C 196 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.198870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165914 restraints weight = 36348.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.166744 restraints weight = 61380.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168318 restraints weight = 54257.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169346 restraints weight = 34648.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.170611 restraints weight = 30001.538| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28686 Z= 0.120 Angle : 0.749 21.603 38752 Z= 0.352 Chirality : 0.046 0.475 4340 Planarity : 0.004 0.081 4770 Dihedral : 14.549 128.065 5226 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 2.63 % Allowed : 22.23 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.14), residues: 3352 helix: -0.32 (0.14), residues: 1418 sheet: -3.20 (0.31), residues: 278 loop : -2.97 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 58 TYR 0.023 0.001 TYR C 86 PHE 0.032 0.001 PHE C 555 TRP 0.055 0.002 TRP D 798 HIS 0.014 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00266 (28634) covalent geometry : angle 0.69653 (38604) SS BOND : bond 0.00191 ( 8) SS BOND : angle 0.73606 ( 16) hydrogen bonds : bond 0.02971 ( 746) hydrogen bonds : angle 4.49718 ( 2130) link_ALPHA1-3 : bond 0.00809 ( 2) link_ALPHA1-3 : angle 3.55311 ( 6) link_ALPHA1-6 : bond 0.00926 ( 2) link_ALPHA1-6 : angle 1.29368 ( 6) link_BETA1-4 : bond 0.00621 ( 14) link_BETA1-4 : angle 3.28347 ( 42) link_NAG-ASN : bond 0.01006 ( 26) link_NAG-ASN : angle 5.65275 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.53 seconds wall clock time: 86 minutes 19.33 seconds (5179.33 seconds total)